Align NatD, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate Ac3H11_1695 High-affinity branched-chain amino acid transport system permease protein LivH (TC 3.A.1.4.1)
Query= TCDB::Q8YXD0 (288 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1695 Length = 309 Score = 147 bits (370), Expect = 4e-40 Identities = 93/306 (30%), Positives = 169/306 (55%), Gaps = 29/306 (9%) Query: 1 MDIQTIQLIVNGIAVGSIIALAAVGLTLTYGILRLSNFAHGDFLTLGAYLTFFVNTFG-- 58 MDI +Q I+NG+ +GS+ AL A+G T+ YGI++L NFAHG+ L +GA ++ + G Sbjct: 1 MDI-LLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSW--SCIGMM 57 Query: 59 ----------VNIWLSMIVAVVGTVGVMLLSEKLLWSRMRSIRANSTTLIIISIGLALFL 108 V + L+ I+A V + + EK+ + +RS + +I +IG+++ L Sbjct: 58 QGAMPGAPGWVILLLATIIACVVAATLNFVIEKVAYRPLRS--SPRLAPLITAIGMSILL 115 Query: 109 RNGIILIWGGRNQNY--NLPITPALDIFGVKVPQNQLLVLALAVLSIGALHYLLQNTKIG 166 + ++IW + Y LP +P +I G + Q+L+L + +++ +L YL+ +T +G Sbjct: 116 QTLAMIIWKPNYKPYPTMLPSSP-FEIGGAFITPTQILILGVTAVALASLVYLVNHTNLG 174 Query: 167 KAMRAVADDLDLAKVSGIDVEQVIFWTWLIAGTVTSLGGSMYGL-ITAVRPNMGWFLILP 225 +AMRA A++ +A + G+ + VI T++I + ++ G MY + MG+ L Sbjct: 175 RAMRATAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLK 234 Query: 226 LFASVILGGIGNPYGAIAAAFIIGIVQEVSTPF--------LGSQYKQGVALLIMILVLL 277 F + + GGIGN GA+ ++G+++ + + + LGS Y A +++I++L Sbjct: 235 AFTAAVFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILT 294 Query: 278 IRPKGL 283 +RP GL Sbjct: 295 LRPSGL 300 Lambda K H 0.328 0.144 0.426 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 261 Number of extensions: 21 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 288 Length of database: 309 Length adjustment: 27 Effective length of query: 261 Effective length of database: 282 Effective search space: 73602 Effective search space used: 73602 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory